Well, here's from the article...
Experts say it is no surprise that HIV circulated in humans for about 70 years before being recognized. An infection usually takes years to produce obvious symptoms, a lag that can mask the role of the virus, and it would have infected relatively few Africans early in its spread, they said.
That seems very possible to me. Let's face it, mysterious lingering maladies are nothing new in sub-Saharan Africa, and early cases of AIDS may have been viewed as variations on one of the many known diseases there. There is a notion in western medicine (completely ignored in the writing of the show "House") -- "You are more likely to see an atypical presentation of a common disease than a typical presentation of a rare disease."
Also, the study of viral diseases progressed relatively little until the 1970s and 1980s, when elctron microscopy and the development of increasingly sophisticated molecular biology tools actually enabled close study of viruses. Prior to this, it was the really obvious viral diseases that could be recognized as such -- influenza, rabies, polio, etc. Retroviruses were essentially undectable using methods developed before the biotech boom of the last few decades.
Even now, new viruses are discovered any time somebody goes looking for them. Most of them are harmless, some may even be beneficial. Conversely, diseases that currently mystify us -- autoimmune diseases, certain types of cancer -- may well have a viral trigger that we haven't stumbled across yet.
It's also possible, I suppose, that HIV existed as a geographically isolated and avirulent strain for its first few decades in human, until random mutation and global travel generated conditions for a more virulent strain to pop up. However, other types of SIV (simian immunodeficiency viruses, of which HIV-1 and HIV-2 are two) typically cause severe disease when they jump outside of their normal host species, so it's difficult to imagine that the first transition into humans didn't cause disease, as well.